<p>Scope 3 greenhouse gas (GHG) emissions and cyber-physical resilience are typically governed through separate institutional and operational frameworks, despite their growing interdependence in digitally mediated supply chains. This separation creates an execution gap that fragments decarbonization, resilience, and investment decisions across data architectures and organizational functions. Grounded in resilience theory and a transdisciplinary systems perspective, this study advances the testable hypothesis that institutional separation of Scope 3 emissions management and cyber-physical resilience is associated with lower system performance, whereas integration through digital governance mechanisms improves operational resilience, emissions measurement accuracy, and financial decision coherence. System performance is operationalized through three dimensions: (1) supply-chain observability and data integration; (2) resilience capacity across the prepare–absorb–recover–adapt cycle; and (3) coherence of investment decision-making under dual materiality. The study applies a structured integrative review with analytical triangulation across sectoral datasets, cyber-risk distributions, and governance frameworks, complemented by an illustrative application in emergency medical services (EMS) in Lithuania. Findings indicate that Scope 3 burdens and cyber-physical risks co-locate in supplier-intensive and digitally dependent sectors, revealing systemic vulnerability; and that effective integration requires a joint governance architecture linking digital observability, standards, financial evaluation, and human-centered decision-making. The article contributes an integrative framework that reframes decarbonization and cyber-physical resilience as a unified systems problem and provides an operational basis for coordinated governance across sustainable supply chains.</p>